All the qiime diversity code should be moved to a subworkflow after PROFILING. Idea is results of profiling should be fed into the diversity subworkflow, so the code doesn't have to be repeated for each profiler. However, I know right now, it only works metaphlan4. So, you could temporarily set the diversity subworkflow to only run when the profiler is metaphlan4.
All the qiime diversity code should be moved to a subworkflow after PROFILING. Idea is results of profiling should be fed into the diversity subworkflow, so the code doesn't have to be repeated for each profiler. However, I know right now, it only works metaphlan4. So, you could temporarily set the diversity subworkflow to only run when the profiler is metaphlan4.